The story begins with DHI (Disney Host Interactive, or Daylight Hologram Imaging) day at the Magic Kingdom. Finn and the other DHIs are riding on a float when Philby (a DHI) notices a gray balloon on the castle. They believe it is a weather balloon, but they're very suspicious. Due to the growing thunderstorm, however, it disappears in the crowd. The kids also notice that Chernabog, a character supposed to be on one of the floats, has gone missing. As the parade continues, Finn sees his old friend Amanda, and her sister Jez (Jess). We learn in this book that the characters have begun to be called Kingdom Keepers because of an adopted name given from a local newspaper. Amanda is trying to warn Finn about something when Charlene notices a pair of monkey-like creatures in the crowd. Jez slows, and Amanda (still trying to warn Finn) puts a leaf to her cheek. Realizing what she means, Finn knows that Maleficent is in the castle.

Together with Philby, the boys go to Escher's Keep and make it to the apartment Wayne (an old Imagineer) had shown them months before. A Dapper Dan, (who Finn immediately guesses as Security) follows the boys up the stairs, Finn trying to trick him by crossing over to his DHI state. Meanwhile the boys are trying to find out what's going on in the castle, Maybeck, Charlene, and Willa go to meet up with Amanda. Amanda realizes that Jez is a matter of fact a DHI, and doesn't know where her real sister went.

Philby and Finn find Maleficent in the castle, who was moved there from the jail-cell from under Pirates of the Caribbean. Maleficent conjures her powers and breaks the bars on the window using the lightning storm, and she flies down the Tinkerbell rope from "Wishes" and flies off to the Animal Kingdom. Finn and Philby rescue the Tinkerbell actress and fly down the rope to Tomorrowland.Being scared they run off. {C
That night, as they await to meet up online, Finn receives an IM from Wayne. Wayne tells him to meet him on a website, DGamer, a private place where VMK is still open (being that VMK closed in the book and in real life.) Wayne talks to Finn on a webcam, and Finn tells him about the nights events. Wayne tells Finn that the Overtakers have managed to clone one of the original, messed-up DHI servers from the first book and hide it somewhere in the Animal Kingdom. The Overtakers are using it to make DHIs out of animals as their army, and if any of the Kingdom Keepers (or Wayne) fall asleep, they will become their DHIs, controlled by the Overtakers' server, and can be put into permanent comas, similar to what happened to Maybeck in the first book. Wayne tells Finn that he and the other Kingdom Keepers must find Jez and destroy the second server in the Animal Kingdom, before they fall asleep and are at the Overtakers' control, and must get to the Animal Kingdom at dawn, before opening, to get into the park. Finn warns the others, and they decide to use their Nintendo DS systems to chat using DGamer and meet up at the Animal Kingdom at dawn. {C

Finn sneaks out of his house at 2 AM, and uses his bike to get to Amanda's house. He discovers that they live alone in an abandoned church. She tells him that she and Jez, who are not really sisters, are Fairlies, which means they are 'fairly human'. They have special powers, but Jez's powers are much more powerful, even more so than Maleficent's, which is why the Overtakers kidnapped her. Finn believes her, promises not to tell, and Amanda also shares that she and Jez grew up in the same orphanage, and both ran away, being that both of their parents died, disappeared or vanished. She also tells Finn that Jez had dreams before, about the future. She drew dreams in her diary, on a page filled with monkeys, a castle being struck by lightning, a sticker, a mountain, other drawings, and the words "CHANGE ROB" written over and over. Finn takes the page, being that it will help them, since the castle being struck by lightning happened the night before. While in the church, Finn and Amanda spy a large bat, suspiciously watching them.

Jess's Journal from KK2

Later, at 4 in the morning, Finn sneaks back into his house and tells his mom he's going to the skate park and it is five in the morning. She believes him, and tells her he will probably go to Blizzard Beach later with his friends. He and the DHIs, along with Amanda, meet up at the Animal Kingdom an hour later. They go into a type of warehouse, and discover that the Dapper Dan who chased Finn and Philby in Escher's Keep is in fact with Wayne. They change into cast members' clothing, Charlene notably dressing up as DeVine, a costumed vine character on stilts. Charlene and Willa discover a bat in the girls' room the size of a bowling pin, the same bat who was at Amanda's apartment. Maybeck catches it, and puts it in a pillowcase. The DHIs set out into the empty park, each as a different person. With Cast Member ID badges, they are free to go anywhere backstage as long as they aren't found out.

In Animal Kingdom, Willa sets out into the jungle, she attempts to go to a feeding place disguised as a stump on the savanna. She is chased and nearly eaten by a dragon-type creature, but is safe once she enters the stump and zebras scare the dragon away. Willa notices that Jess is gone, and 'Change Rob' is written on the wall, just as in Jess's diary. Once the coast is clear, she goes back to the actual park to find Finn.

Maybeck has orders from Finn to put the bat-hostage in the bat enclosure. However, he is attacked by thousands of birds who were stalking him all over. He isn't hurt by them, but the bat is taken away by a monkey. He desperately chases the monkey, following it into the monkey enclosure. However, Maleficent is in the enclosure and stops him and Maybeck is sent running for his life back to Finn.

Philby, at the Conservation Station, has talked to Wayne on VMK and found out how to rig the cameras there and give him security camera access to all the cameras around the park. Charlene, who is posing as the DeVine character, is unseen by everyone, therefore giving her an advantage. She offers to watch the bat enclosure, because Amanda (who is at the Conservation Station) is watching all the cameras she can.
Finn listens to Willa and Maybeck's stories, but all are equally puzzled. At this point, the park has opened to guests, and suddenly, the song "Under the Sea" (sung by Raven Symone) begins playing on the speakers around the park. Amanda is in shock as this is Jess's favorite song, its on her iPod, and this song has never played anywhere in the Animal Kingdom,it's all out of area. Finn and Amanda deduce that Jess must be playing this song from her iPod, and that this must be a clue about something. Willa and Finn each decide to check out this mystery by following the song's clue to other parks.

Finn goes to Disney's Hollywood Studios and heads to the Voyage of the Little Mermaid theater show. While walking in the park, he notices a broomstick character from Fantasia is following him. Finn manages to hide in the show and watch, only to notice the broomstick character stop and study the show. Finn is confused. Meanwhile, Willa has gone to the Magic Kingdom to Ariel's Grotto, a picture station themed to The Little Mermaid. While there, she seems to cause a fuss by asking to open a fake treasure chest in the area, thinking it might contain something. It is revealed to be empty, and Willa is pushed away by a cast member, who remarks that a Captain Hook costumed character had also tried to do the same thing earlier.

Finn and Willa reunite at the Animal Kingdom, and realize that the Overtakers must have heard the song and been trying to follow the clues too, perhaps to find Jez.
Jez is eventually found inside the Animal Kingdom's tiger enclosure, and the DHIs must hurry to Expedition Everest to stop Maleficent from releasing Chernabog, using the final clue in Jez's diary. By the time they get to the attraction, the park has closed to guests, and the kids scale into the empty climactic end of the attraction. However, they are too late as Maleficent releases Chernabog from his trapped form as the animatronic ride Yeti. Chernabog tries to kill Finn, when Amanda saves him and the kids escape in an oncoming ride car. In the end, the Kingdom Keepers have failed to stop the Overtakers, who have reportedly hid away in Disney's Hollywood Studios in the back of an ice truck. The kids decide they must quickly find the stonecutter's quill if they want to regain leverage against the Overtakers, who have most likely been the cause of Wayne's sudden and mysterious disappearance.